RNA Shows Design, Too

RNA differs from DNA in one of the sugars that makes up its backbone and one of the bases that makes up its side branches (uracil instead of thymine); it is also usually found in single strands instead of DNA's double helix. New discoveries, though, are showing RNA does far more than passively transfer DNA's information to other places. It, too, is a masterpiece of intelligent design and function.

A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structuredin vivo, and we show for three examples that these structures affect protein expression."

In other words, the structure, not just the sequence, carries functional information. "Our studies provide an excellent set of candidate regions, among the truly enormous number of structured regions seen in vitro, for exploring the regulatory role of structured mRNAs."

Two other papers in the same issue, by Ding et al. and Wan et al., augment the theme with additional findings of regulatory information in RNA structure. In the accompanying News & Views article in Nature, two geneticists from the University of North Carolina call this "a second layer of information in RNA." Wan et al. agree, "In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure."

The difficulty of putting two layers of information on a single strand can be appreciated with a thought experiment: design a rope studded with magnets that conveys a message in the sequence of magnets. Then, design it in such a way that it folds up into a shape that also conveys a message. That would be a neat trick.

As Casey Luskin reported last month, another form of RNA molecules, long intergenic noncoding RNAs (lincRNAs), are no longer considered "junk." Since then, a news release from Harvard has emphatically agreed, saying of these lincRNAs, "Much of what had been dismissed in fact plays as vital a role as protein-coding genes." Now that the junk glasses are off, science can advance under a design paradigm. "It's likely that in the future we'll see a number of studies showing that other lincRNAs are involved in specific behaviors," one of the researchers says. "The brain likes this junk RNA."

If RNAs show design, why not design them ourselves? In an experimental twist, researchers at Carnegie Mellon invited the public to be their design lab. In a "crowdsourcing" experiment, they found that volunteers could create new RNA designs better than computers could. The starting pool of 37,000 citizen scientists has grown to 130,000 members exercising their intelligent design skills.

An enthusiastic group of non-experts, working through an online interface and receiving feedback from lab experiments, has produced designs for RNA molecules that are consistently more successful than those generated by the best computerized design algorithms, researchers at Carnegie Mellon University and Stanford University report.

The paper in PNAS describes how they succeeded in finding new "RNA design rules" in a "massive open laboratory." The authors report, "These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science."

More design found in what was formerly called junk; more information found parallel to existing information in RNA; more power found in the collective energy of intelligent agents. Why are you not surprised?